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1. A chemostat-based model for growing bacterial biofilms

   https://doi.org/10.1128/spectrum.02333-25  

   Spagnolo, Fabrizio; Caballero, Iñigo; Goldblatt, Alexandra; Loccisano, Michael J; Mahe, Mazharul I; Mejia, Yaxkyn; Melvani, Naya; Nagel, Aliza; Stanciu, Aiden; Kannoly, Sherin; et al (December 2025, Microbiology Spectrum)

   Khursigara, Cezar M (Ed.)

   ABSTRACT Biofilms are groups of microbes that live together in dense communities, often attached to a surface. They play an outsized role in all aspects of microbial life, from chronic infections to biofouling to dental decay. In recent decades, appreciation for the diversity of roles that biofilms play in the environment has grown. Yet, most bacterial studies still rely upon approaches developed in the 19th century and center on planktonic populations alone. Here, we present a chemostat-based experimental platform to investigate not only biofilms themselves but how they interact with their surrounding environments. Our results show that biofilms grow to larger sizes in chemostats as opposed to flasks. In addition, we show that biofilms may be a consistent source of migrants into planktonic populations. We also show that secondary biofilms rapidly develop although these may be more susceptible to environmental conditions. Taken together, our data suggest that chemostats may be a flexible and insightful platform for the study of biofilmsin vitro.IMPORTANCEBiofilms are the predominant way that bacteria live in natural environments and are characterized by three emergent properties: ubiquity, resilience, and impact. They can be found across all environments, both natural and human-made, and across all of recorded time, dating back at least 3.5 billion years. Biofilms also represent a major economic impact of over $5 trillion annually. Yet, most of what is known about bacteria is the result of studies using planktonically growing liquid cultures under laboratory conditions. Here, we propose a comprehensive experimental platform that allows for study of biofilms on the molecular, organismal, and community levels using chemostats. 

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2. Biosynthetic gene clusters in Pseudomonas viridiflava have a fitness cost during Arabidopsis thaliana infection

   https://doi.org/10.1128/msystems.00212-26  

   Duque-Jaramillo, Alejandra; Symeonidi, Efthymia; Neumann, Manuela; Ashkenazy, Haim; Allen, Madelyn; Weigel, Detlef; Karasov, Talia L (June 2026, mSystems)

   Kovács, Ákos T (Ed.)

   ABSTRACT Specialized or secondary metabolites mediate biotic interactions, including virulence and defense. In plant-pathogenicPseudomonas, certain specialized metabolites can enhance colonization of plant hosts, yet their broader contribution to plant–microbe interactions and the relative importance of different metabolites remain unclear. Specialized metabolites are products of enzymes encoded in biosynthetic gene clusters (BGCs), whose prediction from genome sequences has become routine but whose functional roles are rarely tested experimentally. Here, we characterize the BGC repertoire of 225P. viridiflavaisolates fromArabidopsis thalianaand assess BGC contributions to fitness and disease severityin planta. The BGC landscape ofP. viridiflavawas dominated by non-ribosomal peptide synthetase (NRPS) and NRPS-like BGCs, which accounted for 50% of the predicted BGCs. One-third of the BGC families were restricted to a single isolate. Transposon mutagenesis coupled with random barcode transposon sequencing (RB-TnSeq) revealed that the majority of BGCs reduce rather than increase fitness duringA. thalianainfection, with the magnitude of the fitness cost varying across host genotypes. This cost could be due to exploitation of public goods by cheater mutant strains. In single-isolate plant infections, where public goods are not available, we found 11/34 BGC families correlated with disease severity. Yet, only two of these (an N-acetylglutaminylglutamine amide [NAGGN] and an NRPS) were negatively associated with disease severity, which is positively correlated with bacterial growth in this pathosystem, further indicating that BGCs are generally not beneficialin planta. Our findings reveal extensive and largely uncharacterized biosynthetic potential in populations ofP. viridiflavaand indicate that candidate metabolites are likely not adaptive for direct interactions with the plant, but perhaps for microbe-microbe interactions eitherin plantaor in other ecological niches. IMPORTANCEBacteria, including plant-associated bacteria such asPseudomonas viridiflava, produce a vast array of chemical compounds, called secondary or specialized metabolites, that can mediate their interaction with the plant host or other microorganisms. Some of these compounds are known to directly influence how bacteria interact with plants, but it has been unclear whether this is a general rule. We studied a large collection of closely related leaf-dwellingP. viridiflava—a plant pathogen—that varied in their ability to cause disease. We found that very few of the gene clusters responsible for making specialized metabolites improved the ability of the bacteria to colonize its natural hostArabidopsis thaliana. On the contrary, carrying these gene clusters often reduced bacterial growth and disease severity in plants. Specialized metabolites may instead primarily be important for interacting with other microbes, different host species, or under environmental conditions we did not test. These are questions that remain for future research. 

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3. Overcoming toxicity: How nonantagonistic microbes manage to thrive in boom-and-bust environments

   https://doi.org/10.1073/pnas.2424372122  

   Wang, MingYi; Vladimirsky, Alexander; Giometto, Andrea (July 2025, Proceedings of the National Academy of Sciences)

   Antagonistic interactions are critical determinants of microbial community stability and composition, offering host benefits such as pathogen protection and providing avenues for antimicrobial control. While the ability to eliminate competitors confers an advantage to antagonistic microbes, it often incurs a fitness cost. Consequently, many microbes only produce toxins or engage in antagonistic behavior in response to specific cues like quorum sensing molecules or environmental stress. In laboratory settings, antagonistic microbes typically dominate over sensitive ones, raising the question of why both antagonistic and nonantagonistic microbes are found in natural environments and host microbiomes. Here, using both theoretical models and experiments with killer strains ofSaccharomyces cerevisiae, we show that “boom-and-bust” dynamics—periods of rapid growth punctuated by episodic mortality events—caused by temporal environmental fluctuations can favor nonantagonistic microbes that do not incur the growth rate cost of toxin production. Additionally, using control theory, we derive bounds on the competitive performance and identify optimal regulatory toxin-production strategies in various boom-and-bust environments where population dilutions occur either deterministically or stochastically over time. Our mathematical investigation reveals that optimal toxin regulation is much more beneficial to killers in stochastic, rather than deterministic, boom-and-bust environments. Overall, our findings show how both antagonistic and nonantagonistic microbes can thrive under varying environmental conditions. 

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4. Quantification of the coupled dynamics of marine microbes and reactive oxygen species in laboratory batch culture experiments

   https://doi.org/10.1128/spectrum.00712-25  

   McCullough, Donna K; Bowden, Emily C; Calfee, Benjamin C; Gilchrist, Michael A; Zinser, Erik R; Talmy, David (June 2026, Microbiology Spectrum)

   Hom, Erik_F Y (Ed.)

   ABSTRACT Prochlorococcus, the smallest and most numerous phytoplankter of the oligotrophic surface ocean, is vulnerable to damage by the reactive oxygen species hydrogen peroxide (H₂O₂). The most harmful effects of exogenous H₂O₂are mitigated by detoxifying organisms, but even at low concentrations, the ecological and biogeochemical consequences of H₂O₂damage are not fully understood. Here, we present coupled ordinary differential equation models of the dynamics of diverse marine microbes grown in different levels of H₂O₂. We fit our model to monoculture time-series data of peroxide-sensitiveProchlorococcusand peroxide-resistantSynechococcus, picoeukaryotes, and bacteria. Our fits provide estimates of H₂O₂cell damage and detoxification rates in these ecologically important microbes. We find significant variation in rates of cell death and H₂O₂detoxification by taxonomy and H₂O₂concentration. Picoplankton (Micromonasspp. orOstreococcusspp.) and other previously investigated heterotroph helpers (Alteromonas) appear to upregulate detoxification when H₂O₂is elevated, whereasSynechococcusdetoxification rate does not vary with hydrogen peroxide concentration. As expected, elevated H₂O₂is damaging to high light-adaptedProchlorococcus, but they are capable of modest detoxification when H₂O₂concentration is relatively low. Our use of differential equation models to quantify parameters underlying microbe-H₂O₂dynamics provides a basis for ecosystem models to explore the impact of reactive oxygen species on cell mortality of different ocean microbes and computational exploration of H₂O₂impacts on microbial community composition. IMPORTANCEHydrogen peroxide produced naturally in the surface ocean is toxic to many abundant microbes that perform important ecosystem services such as carbon fixation. Much of the naturally occurring hydrogen peroxide produced in the surface ocean is detoxified by “helper” organisms. The healthy function of microbial communities may therefore depend upon the presence of different helpers. Mathematical models provide an important means to evaluate the impacts of hydrogen peroxide on ecosystem function. This study introduces a framework to evaluate the sensitivity of diverse microbes to hydrogen peroxide, in a manner that is amenable for inclusion in ecosystem models. It lays a foundation for future efforts to evaluate the impact of hydrogen peroxide on ecosystem function and microbial community composition. 

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5. Dissolved oxygen concentrations influence microbial community structure and key players in an oxygen minimum zone

   https://doi.org/10.1128/msphere.00751-25  

   Dombroski, Kaitlin R; Campbell, Lauren G; Morris, Robert M; Mason, Olivia U (August 2026, mSphere)

   Lahmers, Kevin K (Ed.)

   ABSTRACT Oxygen minimum zones (OMZs) are expanding in the global ocean. Declining oxygen can alter microbial processes that regulate carbon, nitrogen, and sulfur cycling, including pathways with the potential to produce nitrous oxide (N₂O), a potent greenhouse gas. Yet, we lack a full understanding of how microbial communities respond to declining oxygen in some globally important OMZs. This is particularly true for the understudied northern Benguela Upwelling System (nBUS), an important source of marine N₂O. Here, we analyzed the influence of oxygen concentrations on microbial communities in the nBUS OMZ using 16S rRNA gene sequence data. Microbial diversity did not decline linearly with oxygen and was highest under dysoxic (0.2–2.0 mL/L) conditions and lowest under suboxic (0.0–0.2 mL/L) conditions. This pattern was primarily due to changes in community evenness, which decreased in suboxic samples as the relative abundance ofThioglobaceae(SUP05) increased.Thioglobaceaerelative abundance was significantly inversely correlated with oxygen, andThioglobaceaewere abundant in the nBUS OMZ. Analysis of 216 publicly available medium- to high-qualityThioglobaceaegenomes from cultured and uncultured microbes sampled in the nBUS and other OMZs revealed the metabolic potential of this clade for carbon fixation and consumption, sulfur oxidation, and denitrification. Importantly, fewThioglobaceaepossess the genetic potential to carry out complete denitrification as most lack the gene that converts N₂O to dinitrogen gas. As OMZs expand in size and severity, decreasing microbial diversity and a concomitant increase in the relative abundance ofThioglobaceaecould contribute to enhanced N₂O production through incomplete denitrification.IMPORTANCEMarine microbes mediate biogeochemical cycles, which are influenced by oxygen concentrations, including microbial pathways that can lead to nitrous oxide (N₂O) production. The oxygen minimum zone (OMZ) in the northern Benguela Upwelling System (nBUS) is a biogeochemical hotspot and an important source of nitrous oxide. Yet, microbial community responses remain poorly characterized in this understudied OMZ. Analysis of microbial communities in this OMZ, combined with comparative genomic analysis ofThioglobaceaefrom the global ocean, revealed that members of this group have the capacity to fix carbon, potentially supporting growth through sulfur oxidation coupled to denitrification. However, fewThioglobaceaehave the genetic potential to carry out complete denitrification, with the final nitrous oxide reduction step often missing. Incomplete denitrification is an important source of N₂O in OMZs. Collectively, this study linked oxygen-associated community shifts in this OMZ to incomplete denitrification in a microbial group that increased in relative abundance as oxygen declined. 

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